#!/bin/bash

set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/o31309_FastqScreen_2024-12-11--13-16-09_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p8001/o31309_FastqScreen_2024-12-11--13-16-09/input_dataset.tsv
LAST_JOB=TRUE
echo "Job runs on `hostname`"
echo "at $SCRATCH_DIR"
mkdir $SCRATCH_DIR || exit 1
cd $SCRATCH_DIR || exit 1
source /usr/local/ngseq/etc/lmod_profile
module add Tools/samtools/1.20 Aligner/Bowtie2/2.5.4 QC/fastp/0.23.4 Tools/kraken/2.1.3 QC/FastQScreen/0.14.1 Dev/R/4.4.0 Tools/Picard/3.2.0

#### NOW THE ACTUAL JOBS STARTS
R --vanilla --slave<<  EOT
EZ_GLOBAL_VARIABLES <<- '/usr/local/ngseq/opt/EZ_GLOBAL_VARIABLES.txt'
if (!library(ezRun, logical.return = TRUE)){
message('retry loading ezRun')
Sys.sleep(120)
library(ezRun)
}
param = list()
param[['cores']] = '4'
param[['ram']] = '15'
param[['scratch']] = '30'
param[['partition']] = 'course'
param[['process_mode']] = 'DATASET'
param[['samples']] = '313091_1-,313092_1-,313093_1-,313094_1-,313095_1-,313096_1-,313097_1-,313098_1-'
param[['paired']] = 'false'
param[['name']] = 'FastqScreen_Result'
param[['nReads']] = '100000'
param[['nTopSpecies']] = '5'
param[['minAlignmentScore']] = '-20'
param[['cmdOptions']] = '-k 10 --trim5 4 --trim3 4 --very-sensitive'
param[['trim_front1']] = '0'
param[['trim_tail1']] = '0'
param[['cut_front']] = 'false'
param[['cut_front_window_size']] = '4'
param[['cut_front_mean_quality']] = '20'
param[['cut_tail']] = 'false'
param[['cut_tail_window_size']] = '4'
param[['cut_tail_mean_quality']] = '20'
param[['cut_right']] = 'false'
param[['cut_right_window_size']] = '4'
param[['cut_right_mean_quality']] = '20'
param[['average_qual']] = '0'
param[['max_len1']] = '0'
param[['max_len2']] = '0'
param[['poly_x_min_len']] = '10'
param[['length_required']] = '18'
param[['cmdOptionsFastp']] = ''
param[['mail']] = ''
param[['sushi_app']] = 'FastqScreenApp'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p8001/o31309_FastqScreen_2024-12-11--13-16-09'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = 'FastqScreen_Result'
output[['Report [File]']] = 'p8001/o31309_FastqScreen_2024-12-11--13-16-09/FastqScreen_Result'
output[['Html [Link]']] = 'p8001/o31309_FastqScreen_2024-12-11--13-16-09/FastqScreen_Result/00index.html'
output[['Order Id [B-Fabric]']] = '31309'
input = '/srv/GT/analysis/course_sushi/public/gstore/projects/p8001/o31309_FastqScreen_2024-12-11--13-16-09/input_dataset.tsv'
EzAppFastqScreen\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r FastqScreen_Result /srv/GT/analysis/course_sushi/public/gstore/projects/p8001/o31309_FastqScreen_2024-12-11--13-16-09/
cd /scratch
rm -rf /scratch/o31309_FastqScreen_2024-12-11--13-16-09_temp$$ || exit 1


echo __SCRIPT END__